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comparison flexbar_split_RR_bcs.xml @ 58:bbbae1ee87e0 draft default tip

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fix for flexbar with small data issue
author rnateam
date Tue, 16 Feb 2016 10:08:58 -0500
parents 25ebec14969a
children
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57:537657678b2b 58:bbbae1ee87e0
12 <requirement type="package" version="2.5">flexbar</requirement> 12 <requirement type="package" version="2.5">flexbar</requirement>
13 </requirements> 13 </requirements>
14 14
15 <version_command>flexbar --version</version_command> 15 <version_command>flexbar --version</version_command>
16 16
17 <command> 17 <command><![CDATA[
18 18
19 flexbar 19 flexbar
20 20
21 --threads \${GALAXY_SLOTS:-1} 21 --threads \${GALAXY_SLOTS:-1}
22 22
47 --barcode-threshold $bThresh 47 --barcode-threshold $bThresh
48 48
49 --max-uncalled $maxUncalled 49 --max-uncalled $maxUncalled
50 --min-read-length $minReadLen 50 --min-read-length $minReadLen
51 51
52 > $output; 52 > $output
53 53
54 mv flexbar_barcode_repA_1.fastq $output_repA_1; 54 && mv flexbar_barcode_repA_1.fastq $output_repA_1
55 mv flexbar_barcode_repA_2.fastq $output_repA_2; 55 && mv flexbar_barcode_repA_2.fastq $output_repA_2
56 mv flexbar_barcode_repB_1.fastq $output_repB_1; 56 && mv flexbar_barcode_repB_1.fastq $output_repB_1
57 mv flexbar_barcode_repB_2.fastq $output_repB_2; 57 && mv flexbar_barcode_repB_2.fastq $output_repB_2
58 58
59 </command> 59 && sleep 20
60
61 ]]></command>
60 62
61 63
62 <inputs> 64 <inputs>
63 65
64 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> 66 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>